Download View Slide Presentation - Association for Pathology Informatics

Informatics Laboratory Digital Imaging Project
APIII 2006
Vancouver, British Columbia
Session F2, Friday, August 18, 2006, 10:30 A.M. to noon
Jules J. Berman, Ph.D., M.D.
Co-chair, Laboratory Digital Imaging Project
President, Association for Pathology Informatics
Purpose of LDIP image specification
1. To permit image users to annotate a pathology image with relevant
technical, pathologic, and clinical information and to convey this
information with the image file.
2. To provide a file that is self-describing, containing well-defined
metadata for all data values, and that uses a standard, generic syntax
that is easy to understand and implement.
3. To produce image files that can be integrated with other image
standards and other types of data expressed in the same syntax.
Specific goals of LDIP
1. Develop an RDF schema for LDIP that employs well-defined
metadata from existing standards (HL7, DICOM, OME, CytometryML,
MISFISHIE, GO).
2. Keep it simple (should not require more than 5 minutes to learn if
you know anything about RDF; 8 minutes if you don't)
3. Publish easily emulated examples of the LDIP schema being used
with HL7, DICOM, jpeg, OME, surgical pathology reports, etc.
4. Follow our progress at: www.ldip.org
Problems with existing standards (including
DICOM)
1. Too complex, hard to understand and implement.
2. Not generic (won't merge with datasets using other standards)
3. Made with non-standard (often obsolete) methodologies (not
XML/RDF, even ascii)
4. Lack the metadata (data descriptors) needed by pathologists.
Arguments for HL7 and DICOM are coercive
1. The U.S. Government is fully backing HL7 and DICOM
2. The major vendors are backing HL7 and DICOM
Shouldn't arguments be based on the scientific or technical merits of the
standards and come from non-conflicted experts with no loyalty to the
standards?
Why governments avoid creating biomedical
standards
Private entities that use a standard may be in the best position to create
the best possible standard.
Private entities are more likely to adopt a new standard if they had a
part in developing the standard.
Governments know that many standards are never adopted by the
public and do not want to waste their resources on a standard that will
be ignored.
Governments may be reluctant to face criticism for standards that may
adversely effect certain segments of its population.
Most importantly, U.S. Government is prohibited by law from
intruding into the Standards development process.
Specified by law:
The National Technology Transfer and Advancement Act of 1995
(NTTAA), Public Law 104-113
This Act directs Federal agencies to use standards developed
by private standards development organizations, instead
of government agencies, whenever feasible.
Industry is not permitted to create coercive
standards:
When industry creates a standard, it should be remembered that every
design element can potentially benefit some entities and harm others.
This is why the standards process can be contentious.
The U.S. RICO laws are invoked as a potential concern for standards
developers.
RICO is the Racketeer Influenced and Corrupt Organizations Act, U.S.
Code Title 18, Part 1, Chapter 96.
From RICO:
(a) Whoever in any way or degree obstructs, delays, or affects
commerce or the movement of any article or commodity in commerce,
by robbery or extortion or attempts or conspires so to do, or commits
or threatens physical violence to any person or property in furtherance
of a plan or purpose to do anything in violation of this section shall
be fined under this title or imprisoned not more than twenty years, or
both.
(b) As used in this section(1) The term "robbery" means the unlawful taking or obtaining of
personal property from the person or in the presence of another,
against his will, by means of actual or threatened force, or violence,
or fear of injury, immediate or future, to his person or property, or
property in his custody or possession, or the person or property of a
relative or member of his family or of anyone in his company at the
time of the taking or obtaining.
(2) The term "extortion" means the obtaining of property from another,
with his consent, induced by wrongful use of actual or threatened force,
violence, or fear, or under color of official right."
Government and Standards Organizations often bet
on the the wrong horse.
From Wikipedia: ISO/OSI
“The model was defined by the International Organization for
Standardization in the ISO standard 7498-1....
Of course, by that time, TCP/IP had been in use for years. TCP/IP was
fundamental to ARPANET and the other networks that evolved into the
Internet.....
Only a subset of the whole OSI model is used today. It is widely
believed that much of the specification is too complicated and that its
full functionality has taken too long to implement, although there are
many people who strongly support the OSI model.
On the other hand, many feel that the best thing about the whole ISO
networking effort is that it failed before it could do too much damage.”
Government and Standards Organizations often bet
on the the wrong horse.
I3C – Dozens of industry and government leaders united to develop
health care interoperability
Sun Microsystems' Informatics Advisory Council
IBM
Apple
Oracle
Federal Government:
National Cancer Institute
National Human Genome Research Institute
Now defunct: Impression is that the group conceded effort to the W3C
which has a generic approach embodied under the semantic web.
LDIP is a way of specifying an image and is not a
standard.
LDIP simply uses generic W3C standards to create a simple way
of expressing image information.
You can basic RDF in a few minutes.
Methods used here can (and should) be extended to other
biomedical domains.
LDIP uses RDF, a existing generic simple syntax
recommended by the W3C
RDF files are collections of statements expressed as data triples
<identified subject><metadata><data>
“Jules Berman” “blood glucose level” “85”
“Mary Smith” “eye color” “brown”
“Samuel Rice” “eye color” “blue”
“Jules Berman” “eye color” “brown”
When you bind a key/value pair to a specified object, you're moving from
the realm of data structure into the realm of data meaning.
RDF permits data to be merged between different files
Medical file:
“Jules Berman” “blood glucose level” “85”
“Mary Smith” “eye color” “brown”
“Samuel Rice” “eye color” “blue”
“Jules Berman” “eye color” “brown”
Merged Jules Berman database:
“Jules Berman” “blood glucose level” “85”
“Jules Berman” “eye color” “brown”
“Jules Berman” “hat size” “9”
Hat file:
“Sally Frann” “hat size” “8”
“Jules Berman” “hat size” “9”
“Fred Garfield” “hat size” “9”
“Fred Garfield” “hat_type” “bowler”
"The image is a squamous cell carcinoma of the floor of the mouth.
It was taken by Jules Berman, on February 2, 2002. The
microscope was an Olympus model 3453. The lens objective was 40x
The camera was a Sony model 342. The image dimensions are
524 by 429 pixels. The microscope and camera were
not calibrated. The specimen Baltimore Hospital Center
S-3456-2001, specimen 2, block 3. The specimen was logged in
8/15/01 and processed using the standard protocol for H&E that
was in place for that day. The patient is Sam Someone, medical
identifier 4357 The tissue was received in formalin. The
specimen shows a moderately differentiated, invasive squamous
carcinoma. The patient has a 30 year history of oral tobacco
use. The image is kept in jpeg (Joint Photographic Experts Group)
file format and named y49w3p2.jpg and kept
in the pathology subdirectory of the hospital's server. It's URL
is https://baltohosp.org/pathology/y49w3p2.jpg The image file
has an md_5 hash value of 84027730gjsj350489 The image has no
watermark Copyright is held by Baltimore Hospital Center, and
all rights are reserved."
[file:image.n3 @prefix :]
[<http://www.pathologyinformatics.org/image_schema.rdf#>.]
[@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>.]
[:Baltimore_Hospital_Center rdf:type "Hospital".]
[:Baltimore_Hospital_Center_4357 rdf:type"Unique_medical_identifier".]
[:Baltimore_Hospital_Center_4357 :patient_name "Sam_Someone".]
[:Baltimore_Hospital_Center_4357 :surgical_pathology_specimen "S3456_2001".]
[:S_3456_2001 rdf:type "Surgical_pathology_specimen".]
[:S_3456_2001 :image <https://baltohosp.org/pathology/y49w3p2.jpg>.]
[:S_3456_2001:log_in_date "2001-08-15".]
[:S_3456_2001 :clinical_history "30_years_oral_tobacco_use".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> rdf:type "Medical_image".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :surgical_pathology_accession_number "S3456-2001".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :specimen "2".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :block "3".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :format "jpeg".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :width "524_pixels".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :height "429_pixels".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :hash_value "84027730gjsj350489".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :hash_type "md_5".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :watermark "none".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :camera "Sony".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :camera_model "342".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :capture_date "2002-02-02".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :diagnosis "squamous_cell_carcinoma".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :topography "floor_of_mouth".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :has "Intellectual_property_restriction".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :copyright "all_rights_reserved".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :copyright_holder "Baltimore_Hospital_Center".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :microscope "Olympus".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :microscope_model "3453".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :microscope_objective_power "40X".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :photographer_name "Jules_Berman".]
Proper triples
“Jules Berman”
A specified object
“blood glucose level”
well-defined metada
“85”
datatyping
1. Unique identifiers for unique objects:
URIs, LSIDs, other identification systems
2. Class identifiers for class objects:
examples.... image class, person class, report class, event class
3. Formal Common Data elements protected in namespaces
example..... chem:blood_glucose ldip:imaging_device
4. Datatyping using xsd for data types
examples.... integer, string literal, one of an enumeration list
CDEs in RDF are either classes or properties. The LDIP model for CDEs
is designed to support automatic transformation into an RDF schema:
The format for classes is:
Class Label (in standard XML tag format, uppercase 1st letter):
Registration Authority: Association for Pathology Informatics
Cardinality: (default is "/[0-9]+/"):
Comment (must include detailed definition):
subClassOf:
Contributor (your consistent first-name last-name):
Date of your contribution (/[\d]{2}\-[\d{2}]\-[\d]{4}]/):
The format for properties is:
Property Label (in standard XML tag format, lowercase 1st letter):
Registration Authority: Association for Pathology Informatics
Cardinality (default is "/[0-9]+/"):
Datatype (can be "literal", a list or a regex; default is "literal"):
Comment (must include detailed definition):
Domain (comma-delimited if multiple):
Range (default is "literal"):
Contributor (your consistent first-name last-name):
Date of your contribution (/[\d]{2}\-[\d{2}]\-[\d]{4}/):
Example: Common Data Element for “Instrument”
Class Label:Instrument
versionInfo (required): 0.1
Registration Authority (required): Association for Pathology Informatics
Language:en
Cardinality (required):/[0-9]+/
Datatype: Literal
comment: All the instruments used in preparing, viewing,
and imaging a specimen. Includes: microscope, camera.
subClassOf:Class
Contributor:Bill Moore
Date_of_contribution:05-15-2006
The plain-text list of CDEs can be automatically converted into RDF schema and
xsd user-defined datatypes.
Summary
Not
1.
to make a new standard for pathology images or to compete with existing
standards.
2. To develop a way for people to specify information about their images using
standard, simple and generic annotation methods.
3. To provide a standard syntax for conveying this information with their image
binaries. The resultant files can be used for telepathology, consultation, posted to
the web, submitted as supplemental material with publications, etc.
4. To integrate terminology from existing healthcare standards (Hl7, DICOM,
OME, others)
5. To provide an infrastructure that can be used by developers as a data exchange
specification that will support interoperability between applications and
standards.